Activity of Topotecan toward the DNA/Topoisomerase I Complex: A Theoretical Rationalization

Abstract

Topotecan (TPT) is a nontoxic anticancer drug characterized by a pH-dependent lactone/carboxyl equilibrium. TPT acts on the covalently bonded DNA/topoisomerase I (DNA/TopoI) complex by intercalating between two DNA bases at the active site. This turns TopoI into a DNA-damaging agent and inhibits supercoil relaxation. Although only the lactone form of the drug is active and effectively inhibits TopoI, both forms have been co-crystallized at the same location within the DNA/TopoI complex. To gain further insights into the pH-dependent activity of TPT, the differences between two TPT:DNA/TopoI complexes presenting either the lactone (acidic pH) or the carboxyl (basic pH) form of TPT were studied by means of molecular dynamic simulations, quantum mechanical/molecular mechanical calculations, and topological analysis. We identified two specific amino acids that have a direct relationship with the activity of the drug, i.e., lysine 532 (K532) and asparagine 722 (N722). K532 forms a stable hydrogen bond bridge between TPT and DNA only when the drug is in its active lactone form. The presence of the active drug triggers the formation of an additional stable interaction between DNA and protein residues, where N722 acts as a bridge between the two fragments, thus increasing the binding affinity of DNA for TopoI and further slowing the release of DNA. Overall, our results provide a clear understanding of the activity of the TPT-like class of molecules and can help in the future design of new anticancer drugs targeting topoisomerase enzymes.

Proton relay network in P450cam formed upon docking of putidaredoxin

“…Then all the restraints were removed and the minimization was continued until convergence criteria were reached. The minimized model system was heated up from 0 to 300 K in a stepwise fashion, following the procedure use in our prior MD studies (seven steps in total) . Backbone atoms of the protein and the camphor ligand were restrained while the system was simulated for 10 ps at 10 K using an NVT ensemble.…”

“…The minimized model system was heated up from 0 to 300 K in a stepwise fashion, following the procedure use in our prior MD studies (seven steps in total). 68,69 Backbone atoms of the protein and the camphor ligand were restrained while the system was simulated for 10 ps at 10 K using an NVT ensemble. The system was simulated for 100 ps at first 50 K and then at 100 K using the same constraints.…”

Personalized medicine of non-gene-specific chemotherapies for non-small cell lung cancer

“…An alternate semi-synthetic derivative of camptothecin is topotecan, which is commonly given with paclitaxel to treat advanced stage NSCLC. Topotecan binds the topoisomerase I enzyme complex to the lesion complex arresting it there and preventing the re-ligation of the DNA strand 45 , 46 , 47 , 48 . The overabundance of arrested topoisomerase I complexes produces an apoptotic effect and eventually, their collision with the replication fork fragments the DNA 45 , 46 , 47 , 48 .…”

“…Topotecan binds the topoisomerase I enzyme complex to the lesion complex arresting it there and preventing the re-ligation of the DNA strand 45 , 46 , 47 , 48 . The overabundance of arrested topoisomerase I complexes produces an apoptotic effect and eventually, their collision with the replication fork fragments the DNA 45 , 46 , 47 , 48 . Known factors of genetic resistance to topotecan rely heavily on efflux pump expression.…”

Proton Relay Network in P450cam is Formed Upon Docking of its Redox Partner Putidaredoxin (Pdx)

“…The minimized model system was heated up from 0 K to 300 K in a stepwise fashion, following the procedure use in our prior MD studies (7 steps in total). [53][54] Backbone atoms of the protein and the camphor ligand were restrained while the system was simulated for 10 ps at 10 K using an NVT ensemble. The system was simulated for 100 ps at first 50 K and then at 100 K using the same constraints.…”